Starting phenix.real_space_refine on Fri Sep 11 18:18:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6vjm_21219/09_2026/6vjm_21219.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vjm_21219/09_2026/6vjm_21219.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vjm_21219/09_2026/6vjm_21219.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vjm_21219/09_2026/6vjm_21219.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6vjm_21219/09_2026/6vjm_21219.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6vjm_21219/09_2026/6vjm_21219.cif" model { file = "/net/cci-nas-00/data/ceres_data/6vjm_21219/09_2026/6vjm_21219.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vjm_21219/09_2026/6vjm_21219.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.008 sd= 0.083 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6837 2.51 5 N 1759 2.21 5 O 1979 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10629 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 684, 5267 Classifications: {'peptide': 684} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 655} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 243 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ARG:plan': 7, 'PHE:plan': 4, 'GLN:plan1': 2, 'ASN:plan1': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 5212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 685, 5212 Classifications: {'peptide': 685} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 656} Chain breaks: 2 Unresolved non-hydrogen bonds: 237 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 192 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 6, 'GLN:plan1': 3, 'ASN:plan1': 4, 'PHE:plan': 2, 'ASP:plan': 2, 'TRP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.85, per 1000 atoms: 0.27 Number of scatterers: 10629 At special positions: 0 Unit cell: (83.16, 106.92, 168.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1979 8.00 N 1759 7.00 C 6837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 220 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 410 " distance=2.03 Simple disulfide: pdb=" SG CYS A 663 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 135 " distance=2.03 Simple disulfide: pdb=" SG CYS B 237 " - pdb=" SG CYS B 266 " distance=2.04 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 302 " distance=2.03 Simple disulfide: pdb=" SG CYS B 553 " - pdb=" SG CYS B 648 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " BETA1-6 " NAG C 1 " - " FUC C 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1006 " - " ASN A 409 " " NAG B1002 " - " ASN B 453 " " NAG C 1 " - " ASN A 440 " " NAG D 1 " - " ASN A 482 " " NAG E 1 " - " ASN A 514 " " NAG F 1 " - " ASN B 404 " Time building additional restraints: 0.98 Conformation dependent library (CDL) restraints added in 402.3 milliseconds 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2566 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 54.0% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 184 through 201 removed outlier: 3.701A pdb=" N GLN A 189 " --> pdb=" O GLY A 185 " (cutoff:3.500A) Proline residue: A 190 - end of helix Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.756A pdb=" N LYS A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 257 removed outlier: 3.521A pdb=" N ALA A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 271 through 276 removed outlier: 3.662A pdb=" N SER A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN A 276 " --> pdb=" O ALA A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.707A pdb=" N LEU A 292 " --> pdb=" O SER A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 293 through 305 removed outlier: 4.043A pdb=" N TRP A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 331 removed outlier: 4.272A pdb=" N THR A 322 " --> pdb=" O VAL A 318 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 334 No H-bonds generated for 'chain 'A' and resid 332 through 334' Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.627A pdb=" N VAL A 351 " --> pdb=" O PRO A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 381 removed outlier: 4.156A pdb=" N LYS A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 419 Processing helix chain 'A' and resid 442 through 454 Processing helix chain 'A' and resid 467 through 485 removed outlier: 4.107A pdb=" N TYR A 471 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP A 472 " --> pdb=" O PRO A 468 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 515 removed outlier: 3.657A pdb=" N SER A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 615 removed outlier: 3.634A pdb=" N VAL A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 644 Processing helix chain 'A' and resid 658 through 693 removed outlier: 4.385A pdb=" N LYS A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE A 685 " --> pdb=" O MET A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 732 removed outlier: 4.264A pdb=" N ASP A 721 " --> pdb=" O LEU A 717 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL A 722 " --> pdb=" O VAL A 718 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LEU A 723 " --> pdb=" O GLY A 719 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 731 " --> pdb=" O ILE A 727 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ASP A 732 " --> pdb=" O TRP A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 791 removed outlier: 3.616A pdb=" N TYR A 789 " --> pdb=" O ILE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 825 removed outlier: 3.781A pdb=" N VAL A 814 " --> pdb=" O TYR A 810 " (cutoff:3.500A) Proline residue: A 821 - end of helix Processing helix chain 'A' and resid 832 through 853 Processing helix chain 'A' and resid 853 through 861 removed outlier: 3.901A pdb=" N MET A 857 " --> pdb=" O PHE A 853 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE A 861 " --> pdb=" O MET A 857 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 91 removed outlier: 3.891A pdb=" N ILE B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Proline residue: B 79 - end of helix Processing helix chain 'B' and resid 109 through 124 Processing helix chain 'B' and resid 135 through 146 removed outlier: 4.105A pdb=" N ILE B 142 " --> pdb=" O VAL B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 165 removed outlier: 4.129A pdb=" N ASP B 165 " --> pdb=" O VAL B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 181 Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.836A pdb=" N TYR B 193 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 220 removed outlier: 3.701A pdb=" N THR B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY B 217 " --> pdb=" O ASN B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 246 removed outlier: 4.004A pdb=" N SER B 239 " --> pdb=" O ASP B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 269 removed outlier: 3.791A pdb=" N ALA B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 262 " --> pdb=" O ASN B 258 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU B 269 " --> pdb=" O CYS B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 292 removed outlier: 3.869A pdb=" N GLU B 291 " --> pdb=" O SER B 288 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 292 " --> pdb=" O TRP B 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 288 through 292' Processing helix chain 'B' and resid 304 through 309 removed outlier: 4.159A pdb=" N ALA B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 removed outlier: 4.227A pdb=" N ARG B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 378 removed outlier: 3.913A pdb=" N ILE B 362 " --> pdb=" O ALA B 358 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TRP B 363 " --> pdb=" O TYR B 359 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLU B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N THR B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 405 removed outlier: 3.931A pdb=" N GLU B 405 " --> pdb=" O ASN B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 509 removed outlier: 4.195A pdb=" N ILE B 484 " --> pdb=" O PRO B 480 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 485 " --> pdb=" O LEU B 481 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE B 490 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLY B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET B 493 " --> pdb=" O THR B 489 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE B 501 " --> pdb=" O SER B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 542 removed outlier: 3.508A pdb=" N PHE B 535 " --> pdb=" O TYR B 531 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU B 539 " --> pdb=" O PHE B 535 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASP B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 541 " --> pdb=" O PHE B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 550 removed outlier: 3.743A pdb=" N PHE B 549 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU B 550 " --> pdb=" O LYS B 547 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 546 through 550' Processing helix chain 'B' and resid 551 through 583 removed outlier: 3.867A pdb=" N VAL B 555 " --> pdb=" O THR B 551 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP B 558 " --> pdb=" O THR B 554 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE B 559 " --> pdb=" O VAL B 555 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS B 574 " --> pdb=" O ALA B 570 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR B 575 " --> pdb=" O MET B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 591 through 619 removed outlier: 3.641A pdb=" N MET B 604 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP B 619 " --> pdb=" O TRP B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 678 removed outlier: 4.023A pdb=" N PHE B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY B 671 " --> pdb=" O LEU B 667 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYS B 672 " --> pdb=" O MET B 668 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TRP B 676 " --> pdb=" O CYS B 672 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU B 677 " --> pdb=" O PHE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 681 No H-bonds generated for 'chain 'B' and resid 679 through 681' Processing helix chain 'B' and resid 691 through 712 removed outlier: 4.573A pdb=" N MET B 702 " --> pdb=" O ASN B 698 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 704 " --> pdb=" O GLY B 700 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 741 removed outlier: 4.384A pdb=" N THR B 733 " --> pdb=" O ILE B 729 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N LEU B 736 " --> pdb=" O SER B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 742 through 748 Processing sheet with id=AA1, first strand: chain 'A' and resid 168 through 175 removed outlier: 3.689A pdb=" N HIS A 216 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 242 removed outlier: 6.082A pdb=" N LEU A 242 " --> pdb=" O LEU A 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 336 through 343 removed outlier: 7.374A pdb=" N ILE A 309 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N GLN A 341 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR A 311 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE A 343 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLN A 313 " --> pdb=" O PHE A 343 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE A 361 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE A 362 " --> pdb=" O PHE A 391 " (cutoff:3.500A) removed outlier: 8.814A pdb=" N ILE A 393 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N GLY A 364 " --> pdb=" O ILE A 393 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N TRP A 390 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N THR A 425 " --> pdb=" O TRP A 390 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LEU A 392 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS A 422 " --> pdb=" O LEU A 542 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ILE A 539 " --> pdb=" O ILE A 550 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 517 through 520 removed outlier: 3.501A pdb=" N PHE A 518 " --> pdb=" O VAL A 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 578 through 583 removed outlier: 3.701A pdb=" N SER A 753 " --> pdb=" O THR A 578 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AA7, first strand: chain 'B' and resid 98 through 105 removed outlier: 8.625A pdb=" N PHE B 131 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N MET B 59 " --> pdb=" O PHE B 131 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N GLN B 153 " --> pdb=" O PHE B 173 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 225 through 230 removed outlier: 3.581A pdb=" N SER B 227 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR B 200 " --> pdb=" O SER B 227 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N THR B 229 " --> pdb=" O THR B 200 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N THR B 202 " --> pdb=" O THR B 229 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 250 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP B 279 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 317 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE B 281 " --> pdb=" O VAL B 317 " (cutoff:3.500A) removed outlier: 9.648A pdb=" N PHE B 319 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N TYR B 314 " --> pdb=" O PHE B 431 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N PHE B 431 " --> pdb=" O TYR B 314 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N GLN B 430 " --> pdb=" O LYS B 438 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS B 438 " --> pdb=" O GLN B 430 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 408 through 410 removed outlier: 3.691A pdb=" N PHE B 408 " --> pdb=" O VAL B 415 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 442 through 443 removed outlier: 3.616A pdb=" N THR B 448 " --> pdb=" O ASN B 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 472 through 474 removed outlier: 6.451A pdb=" N GLN B 473 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N GLU B 646 " --> pdb=" O GLN B 473 " (cutoff:3.500A) 531 hydrogen bonds defined for protein. 1569 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3356 1.35 - 1.47: 2723 1.47 - 1.59: 4711 1.59 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 10874 Sorted by residual: bond pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.17e-02 7.31e+03 9.69e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" C1 NAG A1006 " pdb=" O5 NAG A1006 " ideal model delta sigma weight residual 1.406 1.462 -0.056 2.00e-02 2.50e+03 7.70e+00 bond pdb=" CA VAL A 349 " pdb=" CB VAL A 349 " ideal model delta sigma weight residual 1.534 1.551 -0.016 6.80e-03 2.16e+04 5.82e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.88e+00 ... (remaining 10869 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 14399 2.44 - 4.88: 315 4.88 - 7.32: 50 7.32 - 9.76: 21 9.76 - 12.20: 5 Bond angle restraints: 14790 Sorted by residual: angle pdb=" C THR A 704 " pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta sigma weight residual 121.19 130.65 -9.46 1.59e+00 3.96e-01 3.54e+01 angle pdb=" C GLN A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 121.54 131.41 -9.87 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C GLN A 658 " pdb=" N PHE A 659 " pdb=" CA PHE A 659 " ideal model delta sigma weight residual 120.09 126.20 -6.11 1.25e+00 6.40e-01 2.39e+01 angle pdb=" C ASN B 650 " pdb=" N THR B 651 " pdb=" CA THR B 651 " ideal model delta sigma weight residual 121.54 130.86 -9.32 1.91e+00 2.74e-01 2.38e+01 angle pdb=" C PHE A 645 " pdb=" N PRO A 646 " pdb=" CA PRO A 646 " ideal model delta sigma weight residual 121.91 116.28 5.63 1.35e+00 5.49e-01 1.74e+01 ... (remaining 14785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5656 17.39 - 34.77: 572 34.77 - 52.16: 103 52.16 - 69.55: 21 69.55 - 86.93: 4 Dihedral angle restraints: 6356 sinusoidal: 2374 harmonic: 3982 Sorted by residual: dihedral pdb=" CB CYS B 108 " pdb=" SG CYS B 108 " pdb=" SG CYS B 135 " pdb=" CB CYS B 135 " ideal model delta sinusoidal sigma weight residual -86.00 -24.79 -61.21 1 1.00e+01 1.00e-02 4.98e+01 dihedral pdb=" CB CYS A 663 " pdb=" SG CYS A 663 " pdb=" SG CYS A 761 " pdb=" CB CYS A 761 " ideal model delta sinusoidal sigma weight residual -86.00 -33.83 -52.17 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA THR A 704 " pdb=" C THR A 704 " pdb=" N LEU A 705 " pdb=" CA LEU A 705 " ideal model delta harmonic sigma weight residual -180.00 -150.45 -29.55 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 6353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1403 0.073 - 0.146: 277 0.146 - 0.219: 29 0.219 - 0.292: 2 0.292 - 0.366: 2 Chirality restraints: 1713 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 440 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" C1 NAG A1006 " pdb=" ND2 ASN A 409 " pdb=" C2 NAG A1006 " pdb=" O5 NAG A1006 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" CA PHE A 645 " pdb=" N PHE A 645 " pdb=" C PHE A 645 " pdb=" CB PHE A 645 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1710 not shown) Planarity restraints: 1866 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 320 " 0.045 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO B 321 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 321 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 321 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 467 " -0.036 5.00e-02 4.00e+02 5.32e-02 4.53e+00 pdb=" N PRO A 468 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 468 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 468 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 95 " -0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO B 96 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 96 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 96 " -0.026 5.00e-02 4.00e+02 ... (remaining 1863 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3336 2.82 - 3.34: 9929 3.34 - 3.86: 17923 3.86 - 4.38: 19020 4.38 - 4.90: 31950 Nonbonded interactions: 82158 Sorted by model distance: nonbonded pdb=" OD1 ASP A 721 " pdb=" OH TYR A 776 " model vdw 2.297 3.040 nonbonded pdb=" O ILE B 452 " pdb=" OG1 THR B 455 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 379 " pdb=" OE1 GLU A 414 " model vdw 2.306 3.040 nonbonded pdb=" OG SER A 443 " pdb=" OE1 GLN A 444 " model vdw 2.314 3.040 nonbonded pdb=" O SER A 247 " pdb=" OG SER A 250 " model vdw 2.314 3.040 ... (remaining 82153 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 12.170 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10892 Z= 0.239 Angle : 0.974 18.863 14837 Z= 0.497 Chirality : 0.058 0.366 1713 Planarity : 0.006 0.069 1860 Dihedral : 14.385 86.933 3769 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.19 % Allowed : 10.53 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.38 (0.18), residues: 1357 helix: -2.44 (0.14), residues: 674 sheet: -2.27 (0.35), residues: 182 loop : -3.64 (0.22), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 453 TYR 0.019 0.002 TYR B 663 PHE 0.022 0.002 PHE A 645 TRP 0.015 0.002 TRP B 558 HIS 0.006 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.24 (10874) covalent geometry : angle 0.92971 / 0.49 (14790) SS BOND : bond 0.00253 / 0.19 ( 7) SS BOND : angle 1.82670 / 0.98 ( 14) hydrogen bonds : bond 0.10465 / 7.66 ( 531) hydrogen bonds : angle 6.19622 / 4.26 ( 1569) link_BETA1-4 : bond 0.00784 / 0.41 ( 4) link_BETA1-4 : angle 6.59087 / 3.66 ( 12) link_BETA1-6 : bond 0.00180 / 0.09 ( 1) link_BETA1-6 : angle 3.36015 / 1.73 ( 3) link_NAG-ASN : bond 0.01201 / 0.62 ( 6) link_NAG-ASN : angle 6.23252 / 3.67 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8978 (tt) cc_final: 0.8524 (mp) REVERT: A 178 MET cc_start: 0.8771 (mmt) cc_final: 0.8267 (mmm) REVERT: A 582 LYS cc_start: 0.8865 (tttt) cc_final: 0.8544 (tmtt) REVERT: A 807 MET cc_start: 0.8096 (tpt) cc_final: 0.7843 (tpt) REVERT: B 435 ARG cc_start: 0.9344 (ptp90) cc_final: 0.9143 (mtm-85) REVERT: B 604 MET cc_start: 0.7595 (ptt) cc_final: 0.7312 (ptp) outliers start: 2 outliers final: 1 residues processed: 129 average time/residue: 0.1014 time to fit residues: 19.0056 Evaluate side-chains 90 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 89 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.1980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 261 ASN A 293 HIS A 353 ASN A 508 GLN ** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 HIS B 126 ASN B 192 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 GLN B 401 ASN B 414 GLN B 430 GLN B 503 ASN B 506 ASN B 698 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.071157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.060406 restraints weight = 60547.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061858 restraints weight = 36496.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.062839 restraints weight = 25250.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.063536 restraints weight = 19117.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.064005 restraints weight = 15549.475| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10892 Z= 0.122 Angle : 0.689 13.184 14837 Z= 0.335 Chirality : 0.045 0.366 1713 Planarity : 0.005 0.059 1860 Dihedral : 5.370 26.433 1465 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.52 % Allowed : 13.42 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.21), residues: 1357 helix: -0.71 (0.19), residues: 677 sheet: -2.05 (0.36), residues: 191 loop : -3.21 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 304 TYR 0.021 0.001 TYR B 169 PHE 0.021 0.001 PHE A 645 TRP 0.011 0.001 TRP A 395 HIS 0.003 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 (10874) covalent geometry : angle 0.65578 / 0.33 (14790) SS BOND : bond 0.00194 / 0.14 ( 7) SS BOND : angle 1.13118 / 0.60 ( 14) hydrogen bonds : bond 0.03925 / 2.71 ( 531) hydrogen bonds : angle 4.95907 / 3.44 ( 1569) link_BETA1-4 : bond 0.00589 / 0.30 ( 4) link_BETA1-4 : angle 4.33183 / 2.42 ( 12) link_BETA1-6 : bond 0.00453 / 0.24 ( 1) link_BETA1-6 : angle 2.33004 / 1.21 ( 3) link_NAG-ASN : bond 0.00872 / 0.45 ( 6) link_NAG-ASN : angle 4.88051 / 2.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8994 (tt) cc_final: 0.8650 (mt) REVERT: A 178 MET cc_start: 0.8758 (mmt) cc_final: 0.8205 (mmm) REVERT: A 582 LYS cc_start: 0.8854 (tttt) cc_final: 0.8535 (tmtt) REVERT: A 846 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: B 320 GLU cc_start: 0.8186 (tp30) cc_final: 0.7971 (tp30) REVERT: B 628 TYR cc_start: 0.9031 (t80) cc_final: 0.8577 (t80) outliers start: 27 outliers final: 14 residues processed: 128 average time/residue: 0.0891 time to fit residues: 17.2939 Evaluate side-chains 111 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 529 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 112 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 631 ASN A 658 GLN B 87 GLN B 126 ASN B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.070136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059599 restraints weight = 62732.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.060986 restraints weight = 37924.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061884 restraints weight = 26334.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.062563 restraints weight = 20153.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.062994 restraints weight = 16438.634| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10892 Z= 0.160 Angle : 0.684 12.592 14837 Z= 0.337 Chirality : 0.045 0.352 1713 Planarity : 0.004 0.052 1860 Dihedral : 5.223 36.381 1465 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 2.89 % Allowed : 15.19 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.22), residues: 1357 helix: -0.02 (0.20), residues: 674 sheet: -2.07 (0.34), residues: 210 loop : -2.96 (0.26), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.018 0.002 TYR B 169 PHE 0.021 0.002 PHE A 645 TRP 0.013 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (10874) covalent geometry : angle 0.65425 / 0.33 (14790) SS BOND : bond 0.00260 / 0.20 ( 7) SS BOND : angle 1.12610 / 0.59 ( 14) hydrogen bonds : bond 0.03909 / 2.69 ( 531) hydrogen bonds : angle 4.80564 / 3.35 ( 1569) link_BETA1-4 : bond 0.00476 / 0.24 ( 4) link_BETA1-4 : angle 3.84044 / 2.14 ( 12) link_BETA1-6 : bond 0.00032 / 0.02 ( 1) link_BETA1-6 : angle 2.12429 / 1.08 ( 3) link_NAG-ASN : bond 0.00856 / 0.44 ( 6) link_NAG-ASN : angle 4.77181 / 2.70 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8985 (tt) cc_final: 0.8624 (mt) REVERT: A 178 MET cc_start: 0.8766 (mmt) cc_final: 0.8209 (mmm) REVERT: A 415 MET cc_start: 0.7508 (mmt) cc_final: 0.6933 (mmt) REVERT: A 582 LYS cc_start: 0.8852 (tttt) cc_final: 0.8526 (tmtt) REVERT: A 810 TYR cc_start: 0.7817 (m-80) cc_final: 0.7604 (m-80) REVERT: A 846 TYR cc_start: 0.7423 (OUTLIER) cc_final: 0.6956 (m-80) REVERT: B 403 MET cc_start: 0.9014 (tpt) cc_final: 0.8794 (tpp) REVERT: B 628 TYR cc_start: 0.9066 (t80) cc_final: 0.8700 (t80) outliers start: 31 outliers final: 19 residues processed: 118 average time/residue: 0.0815 time to fit residues: 14.9734 Evaluate side-chains 108 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 11 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 129 optimal weight: 0.1980 chunk 68 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 82 optimal weight: 0.3980 chunk 61 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.070479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.059838 restraints weight = 62225.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.061234 restraints weight = 37490.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.062159 restraints weight = 26031.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.062828 restraints weight = 19944.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.063274 restraints weight = 16319.471| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10892 Z= 0.129 Angle : 0.672 12.474 14837 Z= 0.325 Chirality : 0.045 0.351 1713 Planarity : 0.004 0.050 1860 Dihedral : 5.076 40.812 1465 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 2.80 % Allowed : 16.40 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.23), residues: 1357 helix: 0.23 (0.20), residues: 676 sheet: -1.90 (0.35), residues: 202 loop : -2.88 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.015 0.001 TYR B 663 PHE 0.022 0.001 PHE A 645 TRP 0.011 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (10874) covalent geometry : angle 0.64192 / 0.32 (14790) SS BOND : bond 0.00354 / 0.21 ( 7) SS BOND : angle 2.01455 / 1.17 ( 14) hydrogen bonds : bond 0.03735 / 2.58 ( 531) hydrogen bonds : angle 4.68018 / 3.26 ( 1569) link_BETA1-4 : bond 0.00457 / 0.23 ( 4) link_BETA1-4 : angle 3.48887 / 1.94 ( 12) link_BETA1-6 : bond 0.00153 / 0.08 ( 1) link_BETA1-6 : angle 2.01228 / 1.03 ( 3) link_NAG-ASN : bond 0.00861 / 0.44 ( 6) link_NAG-ASN : angle 4.69435 / 2.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8971 (tt) cc_final: 0.8625 (mt) REVERT: A 178 MET cc_start: 0.8758 (mmt) cc_final: 0.8283 (mmm) REVERT: A 415 MET cc_start: 0.7443 (mmt) cc_final: 0.6931 (mmt) REVERT: A 582 LYS cc_start: 0.8844 (tttt) cc_final: 0.8512 (tmtt) REVERT: A 810 TYR cc_start: 0.7922 (m-80) cc_final: 0.7677 (m-80) REVERT: A 846 TYR cc_start: 0.7384 (OUTLIER) cc_final: 0.6997 (m-80) REVERT: B 320 GLU cc_start: 0.8268 (tp30) cc_final: 0.7986 (tp30) REVERT: B 630 MET cc_start: 0.9378 (pmm) cc_final: 0.9097 (pmm) outliers start: 30 outliers final: 22 residues processed: 117 average time/residue: 0.0786 time to fit residues: 14.6312 Evaluate side-chains 115 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 481 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 37 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 647 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.071018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.060395 restraints weight = 62137.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.061807 restraints weight = 37332.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.062725 restraints weight = 25847.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.063390 restraints weight = 19782.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.063885 restraints weight = 16139.315| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10892 Z= 0.112 Angle : 0.656 12.482 14837 Z= 0.315 Chirality : 0.045 0.349 1713 Planarity : 0.004 0.050 1860 Dihedral : 4.897 42.270 1465 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.82 % Allowed : 16.96 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.23), residues: 1357 helix: 0.41 (0.20), residues: 675 sheet: -1.80 (0.34), residues: 203 loop : -2.81 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 304 TYR 0.025 0.001 TYR A 776 PHE 0.021 0.001 PHE A 645 TRP 0.010 0.001 TRP A 395 HIS 0.004 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10874) covalent geometry : angle 0.62726 / 0.31 (14790) SS BOND : bond 0.00188 / 0.15 ( 7) SS BOND : angle 1.85963 / 1.08 ( 14) hydrogen bonds : bond 0.03544 / 2.44 ( 531) hydrogen bonds : angle 4.55096 / 3.16 ( 1569) link_BETA1-4 : bond 0.00438 / 0.22 ( 4) link_BETA1-4 : angle 3.21438 / 1.79 ( 12) link_BETA1-6 : bond 0.00150 / 0.08 ( 1) link_BETA1-6 : angle 1.88299 / 0.97 ( 3) link_NAG-ASN : bond 0.00868 / 0.45 ( 6) link_NAG-ASN : angle 4.63962 / 2.59 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8999 (tt) cc_final: 0.8637 (mt) REVERT: A 178 MET cc_start: 0.8756 (mmt) cc_final: 0.8275 (mmm) REVERT: A 415 MET cc_start: 0.7347 (mmt) cc_final: 0.6856 (mmt) REVERT: A 582 LYS cc_start: 0.8855 (tttt) cc_final: 0.8509 (tmtt) REVERT: A 846 TYR cc_start: 0.7364 (OUTLIER) cc_final: 0.7095 (m-80) REVERT: B 272 MET cc_start: 0.8861 (mmm) cc_final: 0.8495 (tpp) REVERT: B 459 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: B 630 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.9047 (pmm) REVERT: B 647 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7984 (m-70) outliers start: 41 outliers final: 27 residues processed: 127 average time/residue: 0.0771 time to fit residues: 15.5470 Evaluate side-chains 124 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 93 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 653 HIS Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 647 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 119 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 134 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 353 ASN A 457 HIS B 180 ASN ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 698 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.067498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.057286 restraints weight = 64795.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058591 restraints weight = 39438.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059479 restraints weight = 27581.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.060032 restraints weight = 21113.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.060480 restraints weight = 17507.055| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 10892 Z= 0.292 Angle : 0.803 11.964 14837 Z= 0.402 Chirality : 0.048 0.361 1713 Planarity : 0.005 0.049 1860 Dihedral : 5.425 44.909 1465 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.82 % Allowed : 18.36 % Favored : 77.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.23), residues: 1357 helix: 0.14 (0.20), residues: 671 sheet: -2.03 (0.35), residues: 202 loop : -2.80 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 346 TYR 0.022 0.002 TYR B 663 PHE 0.030 0.003 PHE B 501 TRP 0.025 0.002 TRP B 558 HIS 0.034 0.002 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.29 (10874) covalent geometry : angle 0.77689 / 0.40 (14790) SS BOND : bond 0.00524 / 0.38 ( 7) SS BOND : angle 2.32022 / 1.24 ( 14) hydrogen bonds : bond 0.04522 / 3.15 ( 531) hydrogen bonds : angle 5.05535 / 3.55 ( 1569) link_BETA1-4 : bond 0.00338 / 0.17 ( 4) link_BETA1-4 : angle 3.38289 / 1.88 ( 12) link_BETA1-6 : bond 0.00349 / 0.18 ( 1) link_BETA1-6 : angle 2.15842 / 1.11 ( 3) link_NAG-ASN : bond 0.00958 / 0.50 ( 6) link_NAG-ASN : angle 4.82392 / 2.80 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8839 (mmt) cc_final: 0.8262 (mmm) REVERT: A 582 LYS cc_start: 0.8860 (tttt) cc_final: 0.8507 (tmtt) REVERT: A 846 TYR cc_start: 0.7279 (OUTLIER) cc_final: 0.6864 (m-80) REVERT: B 153 GLN cc_start: 0.8377 (tp40) cc_final: 0.8079 (tp40) REVERT: B 272 MET cc_start: 0.9090 (mmm) cc_final: 0.8446 (tpp) REVERT: B 305 LYS cc_start: 0.9119 (tptt) cc_final: 0.8749 (mptt) REVERT: B 320 GLU cc_start: 0.8325 (tp30) cc_final: 0.8101 (tp30) REVERT: B 403 MET cc_start: 0.9038 (tpt) cc_final: 0.8804 (tpp) REVERT: B 571 MET cc_start: 0.7820 (tpp) cc_final: 0.7409 (tpp) outliers start: 41 outliers final: 34 residues processed: 126 average time/residue: 0.0758 time to fit residues: 15.2115 Evaluate side-chains 122 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 685 ILE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 789 TYR Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 7 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.068673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.058245 restraints weight = 62484.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.059593 restraints weight = 37839.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.060469 restraints weight = 26360.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.061096 restraints weight = 20267.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.061575 restraints weight = 16649.299| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10892 Z= 0.173 Angle : 0.719 12.031 14837 Z= 0.349 Chirality : 0.047 0.353 1713 Planarity : 0.004 0.048 1860 Dihedral : 5.244 43.750 1465 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.63 % Allowed : 19.57 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.23), residues: 1357 helix: 0.25 (0.20), residues: 676 sheet: -2.01 (0.34), residues: 206 loop : -2.68 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 453 TYR 0.018 0.002 TYR A 776 PHE 0.027 0.002 PHE A 645 TRP 0.019 0.001 TRP B 558 HIS 0.005 0.001 HIS B 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.17 (10874) covalent geometry : angle 0.69225 / 0.34 (14790) SS BOND : bond 0.00214 / 0.16 ( 7) SS BOND : angle 1.97766 / 1.05 ( 14) hydrogen bonds : bond 0.04042 / 2.81 ( 531) hydrogen bonds : angle 4.82942 / 3.39 ( 1569) link_BETA1-4 : bond 0.00344 / 0.17 ( 4) link_BETA1-4 : angle 3.09476 / 1.72 ( 12) link_BETA1-6 : bond 0.00133 / 0.07 ( 1) link_BETA1-6 : angle 2.01369 / 1.04 ( 3) link_NAG-ASN : bond 0.00870 / 0.45 ( 6) link_NAG-ASN : angle 4.65966 / 2.64 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8789 (mmt) cc_final: 0.8312 (mmm) REVERT: A 415 MET cc_start: 0.7468 (mmt) cc_final: 0.6882 (mmt) REVERT: A 582 LYS cc_start: 0.8855 (tttt) cc_final: 0.8509 (tmtt) REVERT: A 846 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: B 59 MET cc_start: 0.7778 (pmm) cc_final: 0.7405 (pmm) REVERT: B 153 GLN cc_start: 0.8331 (tp40) cc_final: 0.8006 (tp40) REVERT: B 320 GLU cc_start: 0.8376 (tp30) cc_final: 0.8127 (tp30) REVERT: B 702 MET cc_start: 0.8932 (mmm) cc_final: 0.8655 (mmt) outliers start: 39 outliers final: 30 residues processed: 123 average time/residue: 0.0759 time to fit residues: 14.9491 Evaluate side-chains 119 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 72 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 133 optimal weight: 0.8980 chunk 102 optimal weight: 2.9990 chunk 128 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 432 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.069368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.058983 restraints weight = 62201.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.060340 restraints weight = 37388.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.061237 restraints weight = 25927.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.061878 restraints weight = 19808.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.062297 restraints weight = 16238.349| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10892 Z= 0.143 Angle : 0.703 12.139 14837 Z= 0.337 Chirality : 0.047 0.350 1713 Planarity : 0.004 0.049 1860 Dihedral : 5.106 43.822 1465 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.73 % Allowed : 19.76 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.23), residues: 1357 helix: 0.44 (0.20), residues: 675 sheet: -1.90 (0.34), residues: 203 loop : -2.71 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 453 TYR 0.018 0.001 TYR A 776 PHE 0.026 0.001 PHE A 645 TRP 0.016 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (10874) covalent geometry : angle 0.67871 / 0.33 (14790) SS BOND : bond 0.00262 / 0.20 ( 7) SS BOND : angle 1.52558 / 0.80 ( 14) hydrogen bonds : bond 0.03848 / 2.66 ( 531) hydrogen bonds : angle 4.70188 / 3.29 ( 1569) link_BETA1-4 : bond 0.00367 / 0.19 ( 4) link_BETA1-4 : angle 2.86533 / 1.59 ( 12) link_BETA1-6 : bond 0.00037 / 0.02 ( 1) link_BETA1-6 : angle 1.90396 / 0.99 ( 3) link_NAG-ASN : bond 0.00857 / 0.44 ( 6) link_NAG-ASN : angle 4.62733 / 2.60 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 92 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8768 (mmt) cc_final: 0.8303 (mmm) REVERT: A 415 MET cc_start: 0.7362 (mmt) cc_final: 0.6795 (mmt) REVERT: A 441 MET cc_start: 0.7807 (ttt) cc_final: 0.7407 (tmm) REVERT: A 582 LYS cc_start: 0.8848 (tttt) cc_final: 0.8500 (tmtt) REVERT: A 678 TYR cc_start: 0.6795 (t80) cc_final: 0.6548 (t80) REVERT: A 846 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6940 (m-80) REVERT: B 153 GLN cc_start: 0.8366 (tp40) cc_final: 0.8116 (tp40) REVERT: B 320 GLU cc_start: 0.8400 (tp30) cc_final: 0.8114 (tp30) REVERT: B 571 MET cc_start: 0.7914 (tpp) cc_final: 0.7660 (tpp) REVERT: B 702 MET cc_start: 0.8935 (mmm) cc_final: 0.8675 (mmm) outliers start: 40 outliers final: 34 residues processed: 125 average time/residue: 0.0778 time to fit residues: 15.4348 Evaluate side-chains 123 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 88 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 29 optimal weight: 0.0070 chunk 114 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 113 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 124 optimal weight: 5.9990 overall best weight: 1.9804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.068990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.058600 restraints weight = 62500.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.059950 restraints weight = 37730.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.060691 restraints weight = 26164.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.061396 restraints weight = 20795.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.061835 restraints weight = 16907.196| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10892 Z= 0.163 Angle : 0.720 12.068 14837 Z= 0.346 Chirality : 0.047 0.350 1713 Planarity : 0.004 0.048 1860 Dihedral : 5.112 44.169 1465 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.74 % Favored : 92.26 % Rotamer: Outliers : 3.73 % Allowed : 20.13 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.23), residues: 1357 helix: 0.45 (0.20), residues: 675 sheet: -1.91 (0.34), residues: 204 loop : -2.73 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 453 TYR 0.018 0.001 TYR A 776 PHE 0.027 0.002 PHE A 339 TRP 0.020 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (10874) covalent geometry : angle 0.69583 / 0.34 (14790) SS BOND : bond 0.00279 / 0.21 ( 7) SS BOND : angle 1.44602 / 0.75 ( 14) hydrogen bonds : bond 0.03910 / 2.71 ( 531) hydrogen bonds : angle 4.72426 / 3.31 ( 1569) link_BETA1-4 : bond 0.00321 / 0.16 ( 4) link_BETA1-4 : angle 2.75878 / 1.53 ( 12) link_BETA1-6 : bond 0.00090 / 0.05 ( 1) link_BETA1-6 : angle 1.82152 / 0.94 ( 3) link_NAG-ASN : bond 0.00848 / 0.44 ( 6) link_NAG-ASN : angle 4.65093 / 2.63 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 88 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8782 (mmt) cc_final: 0.8293 (mmm) REVERT: A 415 MET cc_start: 0.7354 (mmt) cc_final: 0.6817 (mmt) REVERT: A 582 LYS cc_start: 0.8853 (tttt) cc_final: 0.8504 (tmtt) REVERT: A 846 TYR cc_start: 0.7348 (OUTLIER) cc_final: 0.6993 (m-80) REVERT: B 153 GLN cc_start: 0.8385 (tp40) cc_final: 0.8133 (tp40) REVERT: B 320 GLU cc_start: 0.8421 (tp30) cc_final: 0.8139 (tp30) REVERT: B 571 MET cc_start: 0.7902 (tpp) cc_final: 0.7624 (tpp) REVERT: B 702 MET cc_start: 0.8932 (mmm) cc_final: 0.8543 (mmt) outliers start: 40 outliers final: 35 residues processed: 121 average time/residue: 0.0760 time to fit residues: 14.7489 Evaluate side-chains 124 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 88 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 100 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.068545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.058253 restraints weight = 62620.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.059590 restraints weight = 37811.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.060479 restraints weight = 26276.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.061018 restraints weight = 20068.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.061512 restraints weight = 16779.288| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10892 Z= 0.184 Angle : 0.744 12.007 14837 Z= 0.357 Chirality : 0.047 0.365 1713 Planarity : 0.004 0.049 1860 Dihedral : 5.204 44.242 1465 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 3.63 % Allowed : 20.22 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.23), residues: 1357 helix: 0.44 (0.20), residues: 670 sheet: -1.86 (0.35), residues: 203 loop : -2.74 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 453 TYR 0.027 0.002 TYR A 810 PHE 0.027 0.002 PHE A 339 TRP 0.023 0.001 TRP B 558 HIS 0.004 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (10874) covalent geometry : angle 0.72120 / 0.35 (14790) SS BOND : bond 0.00296 / 0.22 ( 7) SS BOND : angle 1.41542 / 0.74 ( 14) hydrogen bonds : bond 0.04070 / 2.83 ( 531) hydrogen bonds : angle 4.79154 / 3.36 ( 1569) link_BETA1-4 : bond 0.00278 / 0.14 ( 4) link_BETA1-4 : angle 2.70872 / 1.50 ( 12) link_BETA1-6 : bond 0.00057 / 0.03 ( 1) link_BETA1-6 : angle 1.82124 / 0.94 ( 3) link_NAG-ASN : bond 0.00859 / 0.44 ( 6) link_NAG-ASN : angle 4.67495 / 2.65 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2714 Ramachandran restraints generated. 1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 89 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.8791 (mmt) cc_final: 0.8306 (mmm) REVERT: A 415 MET cc_start: 0.7375 (mmt) cc_final: 0.6834 (mmt) REVERT: A 582 LYS cc_start: 0.8808 (tttt) cc_final: 0.8448 (tmtt) REVERT: A 846 TYR cc_start: 0.7267 (OUTLIER) cc_final: 0.6926 (m-80) REVERT: B 153 GLN cc_start: 0.8454 (tp40) cc_final: 0.8197 (tp40) REVERT: B 320 GLU cc_start: 0.8451 (tp30) cc_final: 0.8174 (tp30) REVERT: B 571 MET cc_start: 0.7975 (tpp) cc_final: 0.7708 (tpp) REVERT: B 702 MET cc_start: 0.8978 (mmm) cc_final: 0.8583 (mmt) outliers start: 39 outliers final: 37 residues processed: 120 average time/residue: 0.0750 time to fit residues: 14.5092 Evaluate side-chains 127 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 89 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 408 ILE Chi-restraints excluded: chain A residue 411 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 645 PHE Chi-restraints excluded: chain A residue 682 PHE Chi-restraints excluded: chain A residue 691 VAL Chi-restraints excluded: chain A residue 734 LEU Chi-restraints excluded: chain A residue 758 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 846 TYR Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 129 MET Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 200 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 445 VAL Chi-restraints excluded: chain B residue 448 THR Chi-restraints excluded: chain B residue 454 ASP Chi-restraints excluded: chain B residue 459 GLN Chi-restraints excluded: chain B residue 468 THR Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 605 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 738 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 42 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 0.0870 chunk 45 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.070474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.059953 restraints weight = 62225.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.061331 restraints weight = 37452.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.062247 restraints weight = 25940.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.062863 restraints weight = 19865.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.063320 restraints weight = 16343.957| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 10892 Z= 0.114 Angle : 0.710 12.300 14837 Z= 0.332 Chirality : 0.046 0.344 1713 Planarity : 0.004 0.049 1860 Dihedral : 4.925 43.519 1465 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 2.89 % Allowed : 21.06 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.23), residues: 1357 helix: 0.61 (0.21), residues: 675 sheet: -1.66 (0.35), residues: 198 loop : -2.71 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 304 TYR 0.017 0.001 TYR A 776 PHE 0.024 0.001 PHE A 339 TRP 0.013 0.001 TRP A 395 HIS 0.005 0.001 HIS A 802 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (10874) covalent geometry : angle 0.68822 / 0.33 (14790) SS BOND : bond 0.00266 / 0.20 ( 7) SS BOND : angle 1.18996 / 0.61 ( 14) hydrogen bonds : bond 0.03591 / 2.47 ( 531) hydrogen bonds : angle 4.51844 / 3.15 ( 1569) link_BETA1-4 : bond 0.00457 / 0.23 ( 4) link_BETA1-4 : angle 2.48610 / 1.37 ( 12) link_BETA1-6 : bond 0.00029 / 0.02 ( 1) link_BETA1-6 : angle 1.57676 / 0.82 ( 3) link_NAG-ASN : bond 0.00854 / 0.44 ( 6) link_NAG-ASN : angle 4.57738 / 2.54 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1582.79 seconds wall clock time: 28 minutes 25.32 seconds (1705.32 seconds total)